TSSpredator - A TSS prediction and classification tool

TSSpredator is a tool for the comparative detection of transcription start sites (TSS) from RNA-seq data. It can integrate data from different experimental conditions but also from different organisms on the basis of a multiple whole-genome alignment.

So far TSSpredator has been successfully applied to many data sets generated using the so-called dRNA-seq protocol by Sharma et al., 2010 1. In addition we have started using it on RNA-seq data produced with the protocol by Ettwiller 2 or Innocenti 3. In this UserGuide we will concentrate on dRNA-seq data, in section Other protocols we will give a short overview of how to use TSSpredator on data produced by that protocols.

Content

• Usage
• Getting started
• Methods
• User Interface
• Settings and Parameters
• Output
• Other protocols
• READemption
• HowTo: example analysis with S.aureus
• HowTo: example analysis with Campylobacter data

Note

This project is under active development.

1

Cynthia M Sharma, Steve Hoffmann, Fabien Darfeuille, Jèrèmy Reignier, Sven Findeiß , Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, et al. “The primary transcriptome of the major human pathogen Helicobacter pylori” Nature, 464(7286):250, 2010.

2

Laurence Ettwiller, John Buswell, Erbay Yigit, and Ira Schildkraut. “A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome”. BMC genomics, 17(1):1-14, 2016.

3

Nicolas Innocenti, Monica Golumbeanu, Aymeric Fouquier d’Hérouel, Caroline Lacoux, Rémy A Bonnin, Sean P Kennedy, Francoise Wessner, Pascale Serror, Philippe Bouloc, Francis Repoila, et al. “Whole-genome mapping of 5 RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis”. Rna, 21(5):1018-1030, 2015.